User: F. Golestan

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F. Golestan20
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Posts by F. Golestan

<prev • 78 results • page 1 of 8 • next >
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Comment: C: Graphical presentation of STRING protein-protein network and gene ontology
... Dear Leite, Thank you so much for your great help and support. That was perfect. Your help and patience is highly appreciated. Best regards. ...
written 1 day ago by F. Golestan20
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Comment: C: DAVID functional Analysis and its visualization of GO terms using Bar plot
... Hello, May I kindly ask you to let me know how can I also add to the above bar chart a vertical red line which shows a threshold (such as for example 0.05 p-value as a threshold of significance). I need to create a bar chart like the attached figure. I assume that the red line, in the attached im ...
written 3 days ago by F. Golestan20
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Comment: C: Graphical presentation of STRING protein-protein network and gene ontology
... Dear Leite, Thank you so much for your great help and guide. Your guides helped me a lot. As you suggested, I used STRING db with my parameters (only experiment, and confidence score of 0.4). I then exported TSV: tab separated values and imported into cytoscape (File -> Import -> Network fro ...
written 4 days ago by F. Golestan20
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protein-protein interaction network
... Hello, I found this paper "https://www.nature.com/articles/s41556-018-0220-2" very useful for my research. I read their paper and supplementary materials. However, in their protein-protein interaction network of Figure 5 ![p-p network][1], I could not understand how they inferred that a protein in ...
network string interaction written 4 days ago by F. Golestan20
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Comment: C: Graphical presentation of STRING protein-protein network and gene ontology
... Dear Leite, Many thanks for your guide. Actually, before, I was using StringApp for pulling ppi networks. But, firstly, by using StingApp, I can not choose to retrieve only experimentally validated interactions (as it is possible in original String database). Secondly, I do not know how to detect "d ...
written 4 days ago by F. Golestan20
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Graphical presentation of STRING protein-protein network and gene ontology
... Hello, I found a paper (https://www.nature.com/articles/s41556-018-0220-2#Fig5) that they created STRING protein-protein network and also gene ontology bar charts as in their Figure 5. ![Fig. 5: Mass spectrometry reveals the distinct reticular adhesome.][1] May I kindly ask you to let me have yo ...
string david interaction-network gene-ontology written 5 days ago by F. Golestan20 • updated 3 days ago by Leite850
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Comment: C: Confusion about FindMarkers(), FindVariableFeatures(), RunTSNE(), and RunUMAP()
... Many thanks for your helpful explanations. I got the points. Thanks a lot. ...
written 6 days ago by F. Golestan20
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Confusion about FindMarkers(), FindVariableFeatures(), RunTSNE(), and RunUMAP() in seurat package
... Hello, I am using Seurat package for the analysis of my single-cell RNA-seq. I read their basic PBMCs tutorial https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html. However, I get confused about some steps. I would highly appreciate having your answers on my following questions: 1) Is FindVari ...
scrna-seq kallisto|bustools seurat written 7 days ago by F. Golestan20 • updated 7 days ago by jared.andrews073.7k
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Comment: C: How to make a loop to run kallisto bus command for so many fastq.gz files at onc
... Thank you very much for your help. I also found another way of doing kallisto bus for many fastq files at once as below: cd /scratch/fsgh1d18/kallisto_bustools_multiple_lanes/fastqs/ kallisto bus -i /scratch/fsgh1d18/kallisto_bustools_multiple_lanes/Mus_musculus.GRCm38.cdna.all.idx -o ...
written 25 days ago by F. Golestan20
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Comment: C: How to make a loop to run kallisto bus command for so many fastq.gz files at onc
... Thanks. The result of running the code with "*_001.fastq.gz" (instead of "*_[R1R2]_001.fastq.gz") is as below: FILEBASE kallisto bus -i /scratch/fsgh1d18/kallisto_bustools_multiple_lanes/Mus_musculus.GRCm38.cdna.all.idx -x 10xv2 -o . -t 16 /scratch/fsgh1d18/kallisto_bustools_multiple_lanes ...
written 27 days ago by F. Golestan20

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